Nucleus

Building a nucleus: First, a sphere with holes...

Put in a little window...

Add some NPCs...

...and there you have it, a nucleus.

A nucleus filled with...stuff.

A typical yeast nucleus...

Nucleus with Nuclear Pore Complex.

Zooming in on a NPC.


Nuclear Pore Complex

NPC cross section, with associated molecules. Black background.

NPC cross section, with associated molecules. White background.

Many NPCs, Andy Warhol style.

NPC with partially transparent surface, side view.

NPC with partially transparent surface, perspective view.

NPC with partially transparent surface, top view.

NPC cross section, with associated molecules. Black background. Grainier texture than above.

NPC bottom view.

NPC core -- FG meshwork.

NPC cross section with associated molecules.
This image was published in a JCB meeting report of the 2002 ASCB meeting.

NPC cross section, with associated molecules.
This image was published in Allen et. al., 2002.

NPC perspective view on white background.

NPC perspective view on black background.

NPC perspective/bottom view on black background.

NPC perspective/top view on black background.

NPC top view on black background.

Shiny NPC side view.

NPC top view, shadow cast on white background.

NPC top view, damaged permeability barrier.

NPC top view, repaired permeability barrier.

NPC side view, shadow cast on white background.

NPCs, black and white.


Transport Factors

A 3D rendering of Ran complexed with the GTP analog GMP-PNP. (PDB ID# 1RRP). Reference: Vetter, I.R., Nowak, C., Nishimoto, T., Kuhlmann, J., Wittinghofer, A. Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport. Nature v398 pp.39-46, 1999.

The yeast Saccharomyces cerevisiae contains 14 karyopherins, many of which are part of the importin b family. The karyopherins can be divided into 3 categories based on their transport direction: importins (for nuclear import), exportins (for nuclear export), and transportins (bidirectional transport). The structure of the mammalian Kap95 homolog, importin b (shown on the right) shows how karyopherins are made up of "HEAT" repeats of tandem anti-parallel alpha helices. Structure Reference: Cingolani, G., Petosa, C., Weis, K., Muller, C.W. Structure of importin-beta bound to the IBB domain of importin-alpha. Nature v399 pp.221-229, 1999.

Karyopherins are defined by 3 types of binding partners: nucleoporins, cargo, and RanGTP. In red is the structure of importin b or Kap95. As shown in green, phenylalanines are central for the binding of nups to the outer grooves of the karyopherin. RanGTP (yellow/orange) and cargo (in this case the IBB domain of importin a, shown in light blue) form more extensive interactions with the interior of the kap. RanGTP causes large conformational changes in the tertiary structure of Kap95 (bottom right). Structure References: (1) Bayliss, R., Littlewood, T., Stewart, M. Structural basis for the interaction between FxFG nucleoporin repeats and importin-beta in nuclear trafficking. Cell v102 pp. 99-108, 2000. (2) Bayliss, R., Littlewood, T., Strawn, L.A., Wente, S.R., Stewart, M. GLFG and FxFG nucleoporins bind to overlapping sites of importin-beta. J Biol Chem v277 pp. 50597-50606, 2002. (3) Liu, S.M., Stewart, M. Structural basis for the high-affinity binding of nucleoporin Nup1 to the Saccharomyces cerevisiae importin-beta homologue, Kap95p. J Mol Biol v349 pp. 515-525. (4) Cingolani, G., Petosa, C., Weis, K., Muller, C.W. Structure of importin-beta bound to the IBB domain of importin-alpha. Nature v399 pp. 221-229, 1999. (5) Lee, S. J., Matsuura, Y., Liu, S.M., Stewart, M. Structural basis for nuclear import complex dissociation by RanGTP. Nature v435 pp. 693-696.


Figures & Models

Nuclear Pore Complexes punctuate the nuclear envelope surrounding the eukaryotic nucleus. Listed on the right is a sampling of the many types of cargo that traverse the NPC to access the nucleoplasm (nuclear import) or the cytoplasm (nuclear export).

Architecture of the NPC. Shown is a model of a prototypical NPC from a side view (left) and top view (right), with dimensions from yeast (in red) or Xenopus (in green). The NPC exhibits 8-fold rotational symmetry, but is asymmetric about the plane of the nuclear envelope. A central framework region serves as a scaffold for the complex, with 8 filaments extending into the cytoplasm to form the cytoplasmic fibrils and 8 more extending into the nucleoplasm and terminating in a ring to form the nuclear basket. The center of the NPC is likely filed with disordered FG nucleoporin domains forming a meshwork.

The NPC is composed of proteins called nucleoporins (nups). The 32 yeast nucleoporins are listed by their subclassifications as pore membrane proteins (POMs), non-FG nups, or FG nups. The list is further divided by the locations of individual nucleoporins within the NPC, which is shown in a cross-sectional graphic on the right.

FG nucleoporins are divided into different subtypes. The various yeast FG nups (shown on the left with each "FG" marked along the length of the nup) approximately localize within the NPC (shown on the right) in correlation with their distinguishing FG subtypes: SAFGxPSFG nups are present in the cytoplasmic fibrils, GLFG nups are present in the central meshwork, and FxFG nups are primarily in the nuclear basket. The FG nup schematic is adapted from Allen, N.P., Huang, L., Burlingame, A., Rexach, M. Proteomic analysis of nucleoporin interacting proteins. J Biol Chem v276 pp. 29268-29274.

Molecular dynamics of Kap95/Kap60-mediated nuclear import of a cNLS-containing cargo. cNLS-cargo binds to Kap60, and Kap60 binds to Kap95 cooperatively to form a trimeric complex. The import complex docks to the NPC at its cytoplasmic face and translocates through to the nucleoplasm, presumably by binding stochastically to FG nups. Nuclear RanGTP then attacks Kap95, releasing Kap60 and cNLS-cargo.

The RanGTP gradient. The asymmetric distribution of the RanGEF and RanGAP activities to the nucleus and cytoplasm (respectively) ensures that Ran is predominately in the GTP-bound form in the nucleoplasm and in the GDP-bound form in the cytoplasm.